Promoter and use thereof

ABSTRACT

The invention discloses a promoter which can be induced to express in acidic conditions, and relates to the field of bioengineering technology. The promoters of the invention are separated from  A. niger  and can actuate and/or regulate the expression of the effectively connected nucleic acids in  A. niger . In the invention the expression of the promoters is studied in  A. niger , and it is indicated that some promoters show weak expression, and some show strong activity. The invention provides an effective method and new thought for organic acids production by fungi or other products produced by fermentation under acidic conditions.

This application claims the benefit of Chinese Patent Application No.201510812316.5, filed on Nov. 20, 2015, which is incorporated byreference for all purposes as if fully set forth herein.

FIELD OF THE INVENTION

The present invention relates to the field of bioengineering technology,and more particularly to a promoter induced in acidic conditions.

DESCRIPTION OF THE RELATED ART

Aspergillus niger is a natural cell factory platform for production oforganic acids and enzymes. Meanwhile, A. niger is considered generallyregarded as safe (GRAS) and has abroad application in future as a hoststrain. A traditional method for strain improvement is mutationbreeding, while the non-rational work makes the screen worktime-consuming and tiring, and it is not necessarily possible to screenout excellent transformants. Several genome-sequencing works of A. nigerwere finished and transcriptome data were analyzed for mechanism oforganic acid production and protein secretion, providing a guide forrational design for aim-product accumulation.

There have already been many successful works on metabolic engineeringof A. niger to improve product synthesis. The mostly used promoters areconstitutive ones, including glyceraldehyde-3-phosphate dehydrogenasepromoter PgpdA of A. nidulans, multiprotein bridging factor 1 Pmbf of A.niger, citrate synthase promoter PcitA of A. niger and pyruvate kinasepromoter Ppki of Trichoderma reesei. All these promoters induce geneexpression from cell-growth-phase, as a result may influence the cellgrowth.

Inducible promoters include glucoamylase promoter Pgla, xylanasepromoter Pxln, Taka-amylase A promoter Pamy, alcohol dehydrogenasepromoter Palc, and Tet-on system and so on. It is necessary to addspecific substrate for inducing gene expression, making these promotersuseful for scientific purposes but uneconomic for industrial purpose.Moreover, the expression strength of these promoters is weaker than thatof the constitutive promoters. Furthermore, the Pxln is inhibited byglucose, while the strength of Pgla is influenced by glucoseconcentration, resulting in the instable expression in medium withglucose as a main carbohydrate.

During the organic acids production by A. niger, for instance citratefermentation, the pH of medium decreases from 5.0 to below 2.0, and apH<3 was essential for citrate synthesis. In order to limit geneexpression during cell-growth-stage but increase expression level duringproduct accumulation stage, it is valuable to find a new kind of acid(low pH) inducible promoter for metabolic engineering of A. niger. Thepromoter could be provided as a regulation tool for dynamic control offermentation, which promotes gene expression naturally as the cellsfinish biomass growing and begin to synthesis product.

SUMMARY OF THE INVENTION

In order to solve the above problems, the invention provides a promoterinduced expression in acidic conditions. By means of the technicalsolutions of the invention, the cell-growth-stage andacid-producing-stage of acid fermentation by A. niger can be naturallyset apart according to pH value, it would be useful of a low pH inducedpromoter for gene expression only at acid-producing-stage. The promoterprovides an effective method and new thought for organic acidsproduction by fungi or other fermentation requiring low pH.

In one aspect, the invention provides a promoter induced in acidicconditions. The promoter has a nucleotide sequence shown in SEQ ID NO.1, or has a nucleotide sequence which is at least 90% homologous withSEQ ID NO. 1, or alternatively has a nucleotide sequence obtained fromSEQ ID NO. 1 by base insertion and/or deletion, which has the sameability to promote or regulate gene expression as SEQ ID NO. 1.

In an embodiment, the promoter has the nucleotide sequence of SEQ ID NO.1, named as Pgas.

In an embodiment, the acidic condition(s)/low pH means an acidenvironment that pH value is approximately equal to 2.0.

In a preferable embodiment, the acidic condition(s)/low pH means an acidenvironment of pH value is less than or equal to 2.0.

In another aspect, the invention also provides use of the promoter ongene expression regulation.

In an embodiment, the use comprises transforming an expression cassettecontaining the promoter into fungi, culturing the fungi in an acidiccondition, and connecting the promoter of the expression cassette to theheterogenous nucleotide sequence such that the hegerogenous nucleotidesequence is regulated by the promoter.

In still other aspect, the invention provides an expression cassettecontaining the promoter.

In a preferable embodiment, the expression cassette contains thepromoter, a heterogeneous nucleotide sequence effectively connected withthe promoter, and a 3′ transcription terminator.

In further still other aspect, the invention provides a transgenicstrain containing the promoter.

In a preferable embodiment, the transgenic strain is obtained bytransforming an expression cassette containing the promoter, aheterogenous nucleotide sequence and a terminator in sequence into ahost cell.

In a more preferable embodiment, the host cell is selected from thegroup consisting of bacteria, algae, fungi, yeast, plants, insects andanimal cells.

In an embodiment, the transgenic strain is constructed by the followingthe steps: (1) obtaining an acid-induced promoter (named Pgas) bysynthesizing or PCR amplification, and constructing a recombinantplasmid by connecting the promoter, the heterogenous gene sequence (thegene to be regulated), and a terminator, Ttrp into an expression vector;(2) obtaining an expression cassette containing the promoter, theheterogenous gene sequence and the terminator in sequence byamplification of the recombinant plasmid, and transforming theexpression cassette into host cells and screening for positive clones,namely, the transgenic strain.

In an embodiment, the host is A. niger and the heterogenous gene is GFP.

In another embodiment, the A. niger strain is H915-1.

By means of the above technical solutions, the invention has thefollowing advantages:

the invention obtains a promoter induced in acidic conditions (low pH)from A. niger successfully, and provides a method for inducing geneexpression in acidic conditions. The invention provides a useful toolfor metabolic engineering of A. niger for organic acid fermentation orfermentation of other products in low pH conditions.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 shows GFP expression under the Pgas and PgpdA promoters in A.niger hyphae at different pH.

FIG. 2 shows GFP fluorescence intensity of transformants at differentpH, wherein gpdA, pth, aat, patI and gas represent transformants withGFP gene expression controlled by PgpdA, Ppth, Paat, PpatI and Pgasrespectively.

DESCRIPTION OF THE PREFERRED EMBODIMENTS

The invention will be further illustrated in more detail with referenceto accompanying drawings. It is noted that, the following embodimentsonly are intended for purposes of illustration and are not intended tolimit the scope of the invention.

Embodiment 1

Genome Extraction from A. niger

Conidia of A. niger (1×10⁶) were inoculated in 100 mL malt extractliquid medium (3% malt extract and 0.5% tryptone) at 35° C. and 250r/min for 48 h. The mycelia were harvested with Miracloth (Calbiochem,San Diego, Calif., USA), washed with sterile water and frozen in liquidnitrogen. Tissues were ground by Liquid nitrogen grinding, and thegenome DNA of A. niger was isolated with a DNeasy Plant Mini Kit(QIAGEN, Germantown, Md., USA).

Embodiment 2

Obtaining Promoters Induced in Acidic Conditions (by Low pH)

A. niger gene expression data (Accession, GSE11725) in NCBI GEO Datasetswere analyzed to detect changes in mRNA levels from pH 4.5 to pH 2.5 and4 genes was identified for increased gene expression with decreased pHvalue. The sequence 1500 bp upstream of the start codon ATG was analyzedusing Neural Network Promoter Prediction software (version 2.2)(http://www.fruitfly.org/seq_tools/promoter.html) and all can beidentified with a transcription start site, and the predicted promoterswere named as Pgas, PpatI, Ppth, and Paat.

Pgas was amplified from the A. niger genome using the primers gas-F (SEQID NO.2) and gas-R (SEQ ID NO.3) with restriction sites Eco RI and Sma Iat the 5′ and 3′ ends, respectively. PpatI was amplified from the A.niger genome using the primers pat-F (SEQ ID NO.4) and pat-R (SEQ IDNO.5) with restriction sites Sac I and Bam HI at the 5′ and 3′ ends,respectively. Ppth was amplified from the A. niger genome using theprimers pth-F (SEQ ID NO.6) and pth-R (SEQ ID NO.7) with restrictionsites Sac I and Bam HI at the 5′ and 3′ ends, respectively. Paat wasamplified from the A. niger genome using the primers aat-F (SEQ ID NO.8)and aat-R (SEQ ID NO.9) with restriction sites Eco RI and Bam HI at the5′ and 3′ ends, respectively.

Primer sequences were as follows:

gas-F (SEQ ID NO. 2):  GAATTCCTGCTCTCTCTCTGCTCTCTTTCTgas-R (SEQ ID NO. 3):  CCCGGGGTGAGGAGGTGAACGAAAGAAGACpat-F (SEQ ID NO. 4): GAGCTCTTAGGAAACCTACCATCCATCGTApat-R (SEQ ID NO. 5): GGATCCTGTGCTGCTTGACTGGACGTTCApth-F (SEQ ID NO. 6): GAGCTCTATGTGTCACGAGTTAGAAAGGApth-R (SEQ ID NO. 7): GGATCCGTGGCCTACATGCTCTGAAACA aat-F (SEQ ID NO. 8):GAATTCCGCTATCTCCATCTGATAGCCATA aat-R (SEQ ID NO. 9):GGATCCGATTGCTTGTCGATTATACAGCGT

Embodiment 3

Construction of Expression Cassette of Promoters Induced in AcidicConditions

GFP (SEQ ID NO.10) was synthesized with coden optimization and containedBam HI and Pst I restriction sites at the 5′ and 3′ ends, respectively.Trp terminator (Ttrp) was PCR amplified with primers Ttrp-F (SEQ IDNO.11) and Ttrp-R (SEQ ID NO.12) using pAN7-1 as a template, andrestriction sites Pst I and Hin dIII was added to the 5′ and 3′ ends,respectively. Ttrp was digested with Hin dIII and Pst I, GFP wasdigested with Bam HI and Pst I, and the two sequence were ligated topUC18 digested with the same enzyme, and pGT was obtained. GFP-Ttrp wasamplified with the primers GFP-F1 (SEQ ID NO.13) and Ttrp-R using pGT asa template and reversely connected to pMD19-T vector (Takara, Tokyo,Japan) to generate pMD-GFP-Ttrp. Pgas and pMD-GFP-Ttrp were digestedwith Eco RI and Sma I and connected to generate the Pgas-GFP-Ttrpexpression vector. For co-transformation, the Pgas-GFP-Ttrp expressioncassette was obtained by PCR with the primers gas-F and Ttrp-R. With thesimilar method, the PpatI-GFP-Ttrp, Paat-GFP-Ttrp, Ppth-GFP-Ttrpexpression cassettes containing the PpatI, Ppth, Paat promotersrespectively were obtained.

For co-transformation, the hygromycin resistant cassette,PgpdA-hph-Ttrp, was obtained by PCR with the primers PgpdA-F (SEQ IDNO.14) and Ttrp-R-2 (SEQ ID NO.15) using pAN7-1 as a template.

Primers:

Ttrp-F (SEQ ID NO. 11):  CTGCAGAGATCCACTTAAACGTTACTGAAATCTtrp-R (SEQ ID NO. 12):  AAGCTTTCGAGTGGAGATGTGGAGTGGGFP-F1 (SEQ ID NO. 13):  GATCCATGGTGAGCAAGG PgpdA-F (SEQ ID NO. 14): CAATTCCCTTGTATCTCTACACACAG Ttrp-R-2 (SEQ ID NO. 15): TCGAGTGGAGATGTGGAGTGG

Embodiment 4

Preparation and Transformation of Protoplast of A. niger

Conidia (3×10⁵/mL) were inoculated in ME medium over night at 200 r/minunder 30° C. The mycelium was harvested via filtration through Miraclothand washed with sterile water. Protoplastation was achieved in thepresence of lysing enzymes in KMC (0.7M KCl, 50 mM CaCl₂, 20 mMMes/NaOH, pH 5.8) for 3 h at 1000 rpm under 37° C. The protoplasts werefiltered through Miracloth and collected via centrifugation at 1,000 rpmunder 4° C. for 10 min and subsequently washed twice with the samevolume STC (1.2 M sorbitol, 10 mM Tris/HCl, 50 mM CaCl₂, pH 7.5), andfinally resuspended in 100 μL STC and directly used for transformation.Ten micrograms of expression cassette (obtained in Example 3) was mixedwith 100 μL STC solution containing at least 10′ protoplasts and 330 μLpolyethylene glycol (PEG) solution (25% PEG 6000, 50 mM CaCl₂, 10 mMTris/HCl, pH 7.5) and kept on ice for 20 min. After mixing with anadditional 2 mL PEG solution and incubating at room temperature for 10min, the protoplast mixture was diluted with 4 mL STC. The aliquots weremixed with 4 mL liquid top agar warmed to 48° C., spread on bottom agarcontaining 150 μg/mL hygromycin, and incubated at 35° C. for 4-7 daysuntil clones appeared. All transformants were purified three times viasingle-colony isolation on the selection medium. The correct integrationwas verified with PCR analysis by using specific genomic primers.

Embodiment 5

Conidia (3×10⁵/mL) of A. niger transformants were inoculated in LBLmedium with different pH (pH at 2.0, 3.0, 4.0 and 5.0) and cultured at35° C. at 120 r/min for 24 h. The samples were checked under amicroscope using blue light to detect the fluorescent of GFP. Wild-typeH915-1 did not show fluorescence at both pH 2.0 and pH 5.0. The PgpdAtransformant showed extremely strong fluorescence intensity at pH 5.0,and strong fluorescence at pH 2.0. The Pgas transformant showed minimalGFP expression at pH 5.0, but enhanced fluorescence intensity at pH 2.0(as shown in FIG. 1.), this indicated that the promoter acts as anacid-enhanced cis-acting element

Relative GFP Fluorescence Strength

The A. niger transformants were cultured at 35° C. for additional 48 h.The pellets were harvested and washed twice with WS buffer (100 mM Tris,pH 7.0) and dried with filter paper immediately. The pellets weretransferred to the MP Lysing Matrix C (MP Biomedicals, Heidelberg,Germany) and the mycelia were disrupted for 3×30 s at 5 m/sec using aFastPrep-24 (MP Biomedicals, New York, N.Y., USA). After centrifugationat 12,000 rpm and 4° C. for 10 min, the supernatant was obtained as aprotein sample. The total protein concentration was determined using theBCA Protein Assay Kit. The protein concentration of each sample wasdiluted to 50 μg/mL and the exact protein concentration (A) wasdetermined. The Cytation 3 Cell Imaging Multi-Mode Reader was used todetect fluorescence with an excitation wavelength of 485 nm and emissionwavelength of 535 nm, and the fluorescence intensity was labeled B. Thestandardized fluorescent intensity was estimated as B divided by A.

As shown in FIG. 2, the fluorescence intensity of PgpdA was strong atdifferent pH, and was set as 100% at pH 5.0. The fluorescence of PgpdAdecreased from pH 5.0 to pH 2.0. Nevertheless, Pgas showed littlefluorescence at pH 3.0, 4.0, and 5.0, but enhanced fluorescence at pH2.0, which was stronger than that of PgpdA at pH 2.0, but weaker thanthat of PgpdA at pH 5.0. The PpatI, Ppth and Paat transformants did notshow significant inducement at low pH.

The above preferred embodiments are described for illustration only, andare not intended to limit the scope of the invention. It should beunderstood, for a person skilled in the art, that various improvementsor variations can be made therein without departing from the spirit andscope of the invention, and these improvements or variations should becovered within the protecting scope of the invention.

What is claimed is:
 1. An expression cassette comprising an isolated promoter having the nucleotide sequence set forth in SEQ ID NO: 1, wherein the expression cassette comprises the isolated promoter, a heterogeneous nucleotide sequence effectively connected with the isolated promoter, and a 3′ transcription terminator.
 2. An expression vector comprising an isolated promoter having the nucleotide sequence set forth in SEQ ID NO: 1, wherein the vector comprises the isolated promoter, a heterogeneous nucleotide sequence effectively connected with the isolated promoter, and a 3′ transcription terminator. 